Biophysics Seminar

semester, 2015


Tuesday, January 20th 2015
2:30 pm:
Biophysics Seminar in 210 Physics
There will be no seminar this week.

Tuesday, January 27th 2015
2:30 pm:
Biophysics Seminar in 210 Physics
Speaker: Elias Puchner, University of Minnesota
Subject: Clustering of a cellular signaling complex provides a mesoscopic hierarchy for tuning pathway gain

Cells have the remarkable ability to accurately sense chemical gradients over a wide range of concentrations. The process of chemotaxis and chemotropism has been extensively studied in the past and it has been shown that adaptation is a crucial feature of the underlying signaling networks. Although many signaling proteins responsible for gradient sensing have been identified, it is unclear whether or how their spatial distribution can modulate pathway activity. Here, we show that spatial clustering of a signaling complex presents an additional regulatory layer that actively tunes pathway gain. We demonstrate that clustering of the signaling complex itself activates the pathway bypassing receptor activation and that the degree of clustering correlates with the adaptive output. Furthermore we identify a negative feedback, which acts on the degree of clustering and which allows adaptation to the input stimulus. Our results may present a general principle of how cells use spatial re-distribution of its signaling proteins as an additional regulatory layer to tune pathway activity.


Tuesday, February 10th 2015
2:30 pm:
Biophysics Seminar in 210 Physics
Speaker: Ben Intoy Department of Physics, Virginia Tech
Subject: Pure and Mixed Strategies in Cyclic Competition

Physicists have been interested in the cyclic competition of species for quite some time. For the first part of my presentation I broadly introduce population dynamics, game theory, and pattern formation observed in spatial systems. I then present the results for when four species compete on different lattice structures. It is found that the probability distributions of the extinction times are non-trivial and contain more information than mean extinction times which are commonly reported in the literature. These non-trivial features have their origin in domain formation of both individual species and alliances and promote coexistence in the system. In the last part of my talk the agents are allowed to have mixed strategies and choose their strategy out of a distribution. This scheme for choosing strategies is not often seen in biology, however it does have applicabilities to economic systems such as the public goods game. This is simulated on a 1D lattice with three and four strategies and interesting patterns and stability properties are found depending on how discretized the choice of strategy of the agents is.


Tuesday, February 17th 2015
2:30 pm:
Biophysics Seminar in 210 Physics
There will be no seminar this week.

Tuesday, February 24th 2015
2:30 pm:
Biophysics Seminar in 210 Physics
Speaker: Yiannis Kaznessis, Department of Chemical Engineering and Material Science
Subject: Multiscale models for antibiotic cellbots

Foodborne gastrointestinal infections are significant causes of morbidity and mortality worldwide. Alarmingly, because of the extensive, non-therapeutic use of antibiotics in agriculture, foodborne bacteria are emerging that are resistant to our most potent drugs.

We will discuss a novel approach to reduce the use of antibiotics in food-producing animals and to treat gastrointestinal infections. We engineer lactic acid bacteria (LAB) that express and release antimicrobial peptides (AMPs). LAB are part of the gastrointestinal microflora and can be safely delivered with known benefits to humans and animals. AMPs are proteins that can be readily produced by LAB. One unique aspect of our approach is the use of synthetic promoters that precisely regulate the delivery of AMP molecules.

At the heart of proposed efforts are multiscale models that guide explanations and predictions of the antagonistic activity of recombinant LAB against pathogenic strains. Models are developed to quantify how AMPs kill bacteria at distinct but tied scales. Using atomistic simulations the various interaction steps between peptides and cell membranes are explored. Mesoscopic models are developed to study ion transport and depolarization of membranes treated with AMPs. Stochastic kinetic models are developed to quantify the strength of synthetic promoters and AMPs expression. We will also present a closure scheme for chemical master equations, providing a solution to a problem that has remained open for over seventy years.1

Experimentally, we engineer lactic acid bacteria to inducibly produce antimicrobial peptides. We have used a library of synthetic biological constructs.2,3 We test these modified bacteria against pathogenic bacteria. We will present results against salmonella and enterococcus.4

1. Smadbeck P, Kaznessis YN. A closure scheme for chemical master equations. Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14261-5. doi: 10.1073/pnas.1306481110.
2. Ramalingam KI, Tomshine JR, Maynard JA, Kaznessis YN. Forward engineering of synthetic bio-logical AND gates, Biochemical Engineering, 47, 38-47, 2009.
3. Volzing K, Billiouris K, Kaznessis YN. proTeOn and proTeOff, New Protein Devices That Inducibly Activate Bacterial Gene Expression, ACS Chemical Biology, 6, 1107-1116, 2011.
4. Volzing K, Borrero J, Sadowsky MJ, Kaznessis YN. Antimicrobial Peptides Targeting Gramnegative Pathogens, Produced and Delivered by Lactic Acid Bacteria. ACS Synth Biol. 2013, 15;2(11):643-50. doi: 10.1021/sb4000367


Tuesday, March 3rd 2015
2:30 pm:
Biophysics Seminar in 210 Physics
There will be no seminar this week.

Tuesday, March 10th 2015
2:30 pm:
Biophysics Seminar in 210 Physics
There will be no seminar this week.

Tuesday, March 17th 2015
2:30 pm:
Biophysics Seminar in 210 Physics
There will be no seminar this week.

Tuesday, March 24th 2015
2:30 pm:
Biophysics Seminar in 210 Physics
There will be no seminar this week.

Tuesday, March 31st 2015
2:30 pm:
Biophysics Seminar in 210 Physics
There will be no seminar this week.

Tuesday, April 7th 2015
2:30 pm:
Biophysics Seminar in 110 PAN
Speaker: Jasmine Foo, School of Mathematics, University of Minnesota
Subject: Evolutionary dynamics in spatially structured populations

In this talk I will present results on a model of spatial evolution on a lattice, motivated by the process of carcinogenesis from healthy epithelial tissue. Cancer often arises through a sequence of genetic alterations. Each of these alterations may confer a fitness advantage to the cell, resulting in a clonal expansion. To model this we will consider a generalization of the biased voter process which incorporates successive mutations modulating fitness, which is interpreted as the bias in the classical process. Under this model we will investigate questions regarding the rate of spread and accumulation of mutations, and study the dynamics of spatial heterogeneity in these evolving populations.


Tuesday, April 14th 2015
2:30 pm:
Biophysics Seminar in 110 PAN
There will be no seminar this week.

Tuesday, April 21st 2015
2:30 pm:
Biophysics Seminar in 110 PAN
Speaker: Dr. Frank Vollmer,Max Planck Institute for the Science of Light, Erlangen, Germany
Subject: Advances in Biodetection with Optical and Mechanical Microresonators

Dr. Frank Vollmer will present his results on advancing chip-scale
biosensing capabilities with optical and mechanical microresonators.
In the optical domain, he has developed a microcavity biosensing
platform that is capable of monitoring single DNA molecules and
their interaction kinetics, hence achieving an unprecedented
sensitivity for label-free detection with light. In the mechanical
domain, he is developing a new force-based biosensing technique
based on the quartz crystal microbalance. By applying centrifugal
forces to a sample, it is possible to repeatedly and
non-destructively interrogate its mechanical properties in situ and
in real time.


Tuesday, April 28th 2015
2:30 pm:
Biophysics Seminar in 110 PAN
There will be no seminar this week.

Tuesday, May 5th 2015
2:30 pm:
Biophysics Seminar in 110 PAN
There will be no seminar this week.

Wednesday, September 9th 2015
10:10 am:
Biophysics Seminar in 110 PAN
There will be no seminar this week.

Wednesday, September 16th 2015
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Gant Luxton (Dept: Genetics, Cell Biology and Development, at UMN
Subject: Dystonia and Defective Nuclear-Cytoskeletal Coupling

The Luxton laboratory is focused on understanding the molecular mechanisms underlying the pathogenesis of dystonia. Dystonia is a neurological movement disorder characterized by repetitive muscle contractions that result in involuntary twisting of the extremities and abnormal posturing. People afflicted with dystonia can experience severe disruptions in their ability to perform routine tasks including walking and sitting. Dystonia is the third most common human movement disorder behind essential tremor and Parkinson’s disease. Despite its prevalence, we understand little about dystonia pathogenesis. The most common and severe form of inherited dystonia is early-onset or DYT1 dystonia. The symptoms of DYT1 dystonia first appear at a mean age of 12.5. DYT1 dystonia is caused by a mutation within the DYT1/Tor1a gene that encodes the evolutionarily conserved torsinA protein resulting in the deletion of a single glutamic acid residue (ΔE302/303, or ΔE). The mechanism through which the ΔE mutation causes DYT1 dystonia is unclear because the basic cellular function of torsinA is unknown. Our research has established torsinA as key regulator of nuclear-cytoskeletal coupling. We study the molecular mechanism of torsinA-dependent nuclear-cytoskeletal coupling using three powerful model systems: wounded fibroblast monolayers, the social amoeba Dictyostelium discoideum, and the Caenorhabditis elegans germline. Our research is holistic as we use biochemical, biophysical, cell biological, molecular genetic, and quantitative imaging approaches. Finally, we are actively screening for small molecules that modulate torsinA function in order to develop novel treatments for DYT1 dystonia.


Wednesday, September 23rd 2015
10:10 am:
Biophysics Seminar in 120 PAN
To be announced.

Wednesday, October 7th 2015
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Wednesday, October 14th 2015
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Sunday, October 18th 2015
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Paul Jardine, Dept. of Diagnostics and Biological Sciences, University of Minnesota
Subject: Role Reversal: Using Biology to Answer Questions in Physics

The broad field of molecular biology originated with the movement of physics into biological systems. With tremendous success, physicists were able to address fundamental questions in biological systems by applying physical methods of analysis. We are attempting to reverse these roles in that we are using a biological system to address complex questions in physics. We study the DNA packaging process in dsDNA viruses. During their assembly, these viruses compact DNA inside a protein shell, or capsid, to near crystalline density. Studying this system allows us to study phenomena not accessible to other experimental systems, including the confinement of charged polymers on the nanometer scale in real time. This work has revealed interesting principles of polymer dynamics, among them the forces that resist DNA confinement, the timescale of relaxation events, and the physical behaviour of molecules as they jam during translocation. I will present a brief overview of this work.


Wednesday, October 21st 2015
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Naomi Courtemanche, University of Minnesota, College of Biological Sciences
Subject: Mechanistic studies of formin-mediated actin assembly

Actin dynamics drive many cellular processes, including motility, cytokinesis and endocytosis. A host of actin-binding proteins controls actin filament nucleation, elongation, capping, branching and bundling. Members of the formin family of proteins nucleate new filaments and remain processively attached to actin filament barbed ends while promoting their elongation. Because we lack many of the details required to understand how formins function in cells, it is not known how they promote healthy cellular proliferation. I will present the results of three studies aimed at elucidating the mechanism of actin polymerization mediated by the S. cerevisiae formin Bni1p. First, I will describe experiments I performed using total internal reflection fluorescence microscopy to address the role of sequence organization in Formin Homology (FH) 1 domain-mediated transfer of profilin-actin to a formin-bound filament end. Second, I will describe a technique I developed called “actin curtains”, which I used to study the effect of linear force on formin-mediated polymerization. I will show that small linear forces dramatically slow formin-mediated polymerization in the absence of profilin, suggesting that force shifts the conformational equilibrium of the end of a formin-bound filament, but that profilin-actin associated with FH1 domains reverses this effect. Third, I will describe the effects of point-substitutions in the FH2 domain on the activity of Bni1p, which suggest that nucleation and elongation are separable functions of formins that involve different interactions with actin. These studies provide insight into the physical properties of formins, which will be useful in guiding future studies aimed at elucidating how sequence variations confer unique biological functions to formin isoforms expressed in the same cell.


Wednesday, October 28th 2015
10:10 am:
Speaker: To be announced
Subject: Recent biophysical papers including technical developments, applications and quantitative biology
Biophysics Journal Club will meet whenever there is no biophysics seminar. The journal club is organized by Elias Puchner and Peter Martin.
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Wednesday, November 4th 2015
10:10 am:
To be announced.
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Wednesday, November 11th 2015
10:10 am:
Speaker: To be announced
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Wednesday, November 18th 2015
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Paul Jardine, Dept. of Diagnostics and Biological Sciences, University of Minnesota
To be announced.

Wednesday, November 25th 2015
10:10 am:
Topic to be announced.
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Wednesday, December 2nd 2015
10:10 am:
To be announced.
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

Wednesday, December 9th 2015
10:10 am:
Biophysics Seminar in 120 PAN
Speaker: Jon Sachs, University of Minnesota
Subject: To be announced.

Wednesday, December 16th 2015
10:10 am:
Speaker: To be announced
10:10 am:
Biophysics Seminar in 120 PAN
There will be no seminar this week.

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